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comparison query.xml @ 10:1af09c5ec0a1 draft

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Uploaded 20180413
author fabio
date Fri, 13 Apr 2018 07:51:29 -0400
parents 8d8a8fe0022e
children ba9d0fc8657f
comparison
equal deleted inserted replaced
9:c144495810c2 10:1af09c5ec0a1
10 python '$__tool_directory__/query.py' 10 python '$__tool_directory__/query.py'
11 11
12 --tree 1 12 --tree 1
13 --search 'rrr' 13 --search 'rrr'
14 --sthreshold ${sthreshold} 14 --sthreshold ${sthreshold}
15 --sort ${sortcontrol}
15 --exact 0 16 --exact 0
16 17
17 #if $conditional_input.inputtype == '0': 18 #if $conditional_input.inputtype == '0':
18 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] ) 19 #set file_paths = ','.join( [ str( $f ) for $f in $conditional_input.txtfiles ] )
19 #if $file_paths is not 'None': 20 #if $file_paths is not 'None':
40 <when value="1"> 41 <when value="1">
41 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the Sequence Bloom Tree that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." /> 42 <param name="sequences" type="text" area="True" size="5x25" label="Manually insert sequences" optional="false" help="Insert a list of (ID, TRANSCRIPT) couples in a tab delimited format, one for each line. The content of this text box will represent a query to the Sequence Bloom Tree that will return a collection containing a file for each ID. The content of these files as result of the tool will be a list of accession numbers." />
42 </when> 43 </when>
43 </conditional> 44 </conditional>
44 <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." /> 45 <param name="sthreshold" size="3" type="float" value="0.7" min="0.0" max="1.0" label="Search threshold" help="This threshold controls the specificity. Lower values will produce more hits to the query. Higher values are more stringent and will produce fewer hits." />
46 <param name="sortcontrol" type="boolean" checked="true" truevalue="1" falsevalue="0" label="Sort the result by the number of hits per transcript." />
45 </inputs> 47 </inputs>
46 <outputs> 48 <outputs>
47 <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection"> 49 <collection name="output_collect" type="list" label="BloomTree Manager - Query result collection">
48 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)" directory="collection_content" ext="auto" /> 50 <discover_datasets pattern="(?P&lt;identifier_0&gt;[^_]+)_(?P&lt;ext&gt;[^_]+)" directory="collection_content" ext="auto" />
49 </collection> 51 </collection>